Wiki

Function

Calculate the isoelectric point of proteins

Description

iep calculates the isoelectric point of a protein from its
amino acid composition assuming that no electrostatic interactions
change the propensity for ionization. Optionally, iep will
plot the ionization curve with respect to pH and write an output file
of the data, where for each pH point the number of bound electrons and
charge is given.

For peptide fragments it is possible to exclude the charges of the
amino and carboxy terminal residues.

Read first file from standard input, write first file to standard output

Boolean value Yes/No

N

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

N

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

N

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

Y

-help

boolean

Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose

Boolean value Yes/No

N

-warning

boolean

Report warnings

Boolean value Yes/No

Y

-error

boolean

Report errors

Boolean value Yes/No

Y

-fatal

boolean

Report fatal errors

Boolean value Yes/No

Y

-die

boolean

Report dying program messages

Boolean value Yes/No

Y

-version

boolean

Report version number and exit

Boolean value Yes/No

N

Input file format

iep reads one or more protein sequences.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.

The input format can be specified by using the
command-line qualifier -sformat xxx, where 'xxx' is replaced
by the name of the required format. The available format names are:
gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
(nbrf), swissprot (swiss, sw), dasgff and debug.

Output file format

With -plot specified, a graphical output is produced.

The output is to the specified graphics device.

The results can be output in one of several formats by using the
command-line qualifier -graph xxx, where 'xxx' is replaced by
the name of the required device. Support depends on the availability
of third-party software packages.

For each pH point it gives the number of bound electrons and the charge.

Data files

iep reads in local data file Epk.dat which contains amino acid
pK values used to calculate the isoelectric point of the whole protein

EMBOSS data files are distributed with the application and stored
in the standard EMBOSS data directory, which is defined
by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

% embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called
".embossdata". Files for all EMBOSS runs can be put in the user's home
directory, or again in a subdirectory called ".embossdata".

Notes

Adjusting the pH of an aqueous protein solution to the point where
the numbers of positive and negative charges on the protein are equal
brings the protein to its isoelectric point. This is often the point
of lowest solubility, presumably because it is the point at which
there are fewest intermolecular repulsions, so that the molecules tend
to form aggregates.

Modified lysines and disulphide bridges affect the contributions of
those residues to the protein charge. A set number of each residue
can be excluded.